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taxnmy> ## get information about Homo sapiens from the
taxnmy> ## packaged taxonomy files
taxnmy> taxdir <- system.file("extdata/taxonomy",package="CHNOSZ")
taxnmy> # H. sapiens' taxonomic id
taxnmy> id1 <- 9606
taxnmy> # that is a species
taxnmy> getrank(id1,taxdir)
Read 63 records
[1] "species"
taxnmy> # the next step up the taxonomy
taxnmy> id2 <- parent(id1,taxdir)
Read 63 records
taxnmy> print(id2)
[1] 9605
taxnmy> # that is a genus
taxnmy> getrank(id2,taxdir)
Read 63 records
[1] "genus"
taxnmy> # that genus is "Homo"
taxnmy> sciname(id2,taxdir)
Read 215 records
[1] "Homo"
taxnmy> # we can ask what phylum is it part of?
taxnmy> id3 <- parent(id1,taxdir,"phylum")
Read 63 records
taxnmy> # answer: "Chordata"
taxnmy> sciname(id3,taxdir)
Read 215 records
[1] "Chordata"
taxnmy> # H. sapiens' complete taxonomy
taxnmy> id4 <- allparents(id1,taxdir)
Read 63 records
taxnmy> sciname(id4,taxdir)
Read 215 records
[1] "Homo sapiens" "Homo" "Homininae" "Hominidae"
[5] "Hominoidea" "Catarrhini" "Simiiformes" "Haplorrhini"
[9] "Primates" "Euarchontoglires" "Eutheria" "Theria"
[13] "Mammalia" "Amniota" "Tetrapoda" "Sarcopterygii"
[17] "Euteleostomi" "Teleostomi" "Gnathostomata" "Vertebrata"
[21] "Craniata" "Chordata" "Deuterostomia" "Coelomata"
[25] "Bilateria" "Eumetazoa" "Metazoa" "Fungi/Metazoa group"
[29] "Eukaryota" "cellular organisms" "root"
taxnmy> ## the names of the organisms in the supplied
taxnmy> ## taxonomy files
taxnmy> taxdir <- system.file("extdata/taxonomy",package="CHNOSZ")
taxnmy> id5 <- c(83333,4932,9606,186497,243232)
taxnmy> sciname(id5,taxdir)
Read 215 records
[1] "Escherichia coli K-12" "Saccharomyces cerevisiae"
[3] "Homo sapiens" "Pyrococcus furiosus DSM 3638"
[5] "Methanocaldococcus jannaschii DSM 2661"
taxnmy> # these are not all species, though
taxnmy> # (those with "no rank" are something like strains,
taxnmy> # e.g. Escherichia coli K-12)
taxnmy> getrank(id5,taxdir)
Read 63 records
[1] "no rank" "species" "species" "no rank" "no rank"
taxnmy> # find the species for each of these
taxnmy> id6 <- sapply(id5,function(x) parent(x,taxdir=taxdir,rank="species"))
Read 63 records
Read 63 records
Read 63 records
Read 63 records
Read 63 records
taxnmy> stopifnot(unique(getrank(id6,taxdir))=="species")
Read 63 records
taxnmy> # note that the K-12 is dropped
taxnmy> sciname(id6,taxdir)
Read 215 records
[1] "Escherichia coli" "Saccharomyces cerevisiae" "Homo sapiens"
[4] "Pyrococcus furiosus" "Methanocaldococcus jannaschii"
taxnmy> ## the complete nodes.dmp and names.dmp files are quite large,
taxnmy> ## so it helps to store them in memory when performing multiple queries
taxnmy> ## (this doesn't have a noticeable speed-up for the small files
taxnmy> ## we use in this example)
taxnmy> taxdir <- system.file("extdata/taxonomy",package="CHNOSZ")
taxnmy> nodes <- getnodes(taxdir=taxdir)
Read 63 records
taxnmy> # all of the node ids in this file
taxnmy> id7 <- nodes$id
taxnmy> # all of the non-leaf nodes
taxnmy> id8 <- unique(parent(id7,nodes=nodes))
taxnmy> names <- getnames(taxdir=taxdir)
Read 215 records
taxnmy> sciname(id8,names=names)
[1] "root" "cellular organisms" "Enterobacteriales"
[4] "Enterobacteriaceae" "Escherichia" "Bacteria"
[7] "Proteobacteria" "Methanococci" "Methanocaldococcus"
[10] "Thermococci" "Thermococcales" "Thermococcaceae"
[13] "Pyrococcus" "Fungi/Metazoa group" "Dikarya"
[16] "Saccharomycotina" "Saccharomycetes" "Saccharomycetales"
[19] "Saccharomycetaceae" "Saccharomyces" "Metazoa"
[22] "Deuterostomia" "Craniata" "Vertebrata"
[25] "Euteleostomi" "Theria" "Euarchontoglires"
[28] "Simiiformes" "Hominoidea" "Homininae"
[31] "Homo" "Archaea" "Sarcopterygii"
[34] "Tetrapoda" "Mammalia" "Eukaryota"
[37] "Eumetazoa" "Bilateria" "Coelomata"
[40] "Amniota" "Escherichia coli" "Chordata"
[43] "Gammaproteobacteria" "Gnathostomata" "Teleostomi"
[46] "Saccharomyceta" "Euryarchaeota" "Pyrococcus furiosus"
[49] "Methanococcales" "Methanocaldococcaceae" "Hominidae"
[52] "Methanocaldococcus jannaschii" "Eutheria" "Haplorrhini"
[55] "Catarrhini" "Primates" "Fungi"
[58] "Ascomycota"
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Up: CHNOSZ examples
Previous: util.units